A 3D mathematical model combining the large eddy simulation turbulent model and discrete phase model is developed to investigate the influence of the stopper rod location on transient flow characteristics and the deposition of inclusions in a bifurcated submerged entry nozzle (SEN). Transient flow characteristics, including the instantaneous flow pattern, jet speed, vertical and horizontal jet angle, and the backflow zone speed and fraction, are quantitatively compared. Transient jet flow characteristics of the left and right SEN port are almost consistent when the stopper rod is ideally centered. When the stopper rod is offset 10 mm, the discrepancy of the jet speed, vertical jet angle, and backflow zone fraction is 0.12 m s−1, 4°, and 4%, respectively. The horizontal angle and backflow speed are primarily affected by the vortex swirling direction at the bottom region of the SEN well. A positive horizontal jet angle is observed under the counterclockwise vortex, resulting in a higher backflow speed. Conversely, a negative horizontal jet angle and a lower backflow speed are observed when the vortex swirling direction is clockwise. The deposition rate of inclusions on the upper SEN wall is much higher when stopper rod is offset.